Knowing the Difference
by Heather Giesbrecht
Summary: When everything has crashed down around you and nothing is the same. Does knowing the difference even matter ? Last in the Difference Trilogy. Chapter 6 - SWAT Posted.
1. Prologue - Letter

_Author's Note:_ Welcome to _Knowing the Difference_.

This is the last story in the _Difference_ Trilogy. Most likely it will be the shortest as well.

_' Italic's ' _- Thoughts **Bold **- **Emphasis.**

* * *

**Prologue - Letter**

Dear Reader,

My name is Neo and I'm just a Rebel now, I was the One - until I found out it was a lie. So many things in my life have been lies lately. This letter detailing how I got to the Machine City could be the last thing I ever write. I don't write it to sound dramatic, it's simply the truth. The leader of the Machines has asked me to record it 'for future reference'.

Those words 'future reference' have given me some hope that I can survive. What do I have to survive you probably wonder ? Answered simply, it would be the fight with my now insane former love, the Ex-Agent A.I named Smith. Complexly, it's so much more than just a fight between Smith and I. It will decide if the Real world, the human city of Zion and Machine-made dream world of the Matrix will survive. Smith has already taken over the Matrix and could try taking over the Machine City now if he wanted. Yet, I know that he won't. I can sense that he's waiting for me, no matter how long writing this takes. Smith has all the time in the world to wait.

What could happen next terrifies me even though I've died before. For you to actually understand that I should stop stalling. I will record the last two days until now - all the encounters, thoughts and dreams I remember. The only way I can do that without loosing my nerve is in third-person, bear with me.


	2. Chapter 1 - Planning

**Planning**

Two days ago...

Neo looked around at the dull metal walls and table of the Nebuchadnezzar's dining-room, at the three Captains'. Tall, short-black haired and dark-skinned Niobe of the Logos. She had arrived earlier this morning with her First-Mate Ghost and Operator Sparks. Shorter and pale-skinned Ballard of the Caduceus, who had been with them for the past few days. Along with his own dark-skinned and bald Captain, Morpheus of the Neb. He didn't want to risk the other Captains, Morpheus and his fellow crew-members said they'd help.

He pushed long black-hair out of his eyes, then asked " Niobe, Ballard. Are you sure you want to help us tonight ? You can still back out. Especially, you Ballard after the Bane-Smith ... incident. "

_'If Trinity and Morpheus can take out the Nuclear Plant's Reactor... Niobe wouldn't have to risk herself and Ghost. Plus I would have time to get into the Matrix's Source with Switch and the Keymaker. We're __**so**__ close to ending the war, Zion could be safe in just a few hours.'_

The Caduceus's Captain replied " Neo, you need all the help you can get. I talked to Malachi earlier, he's fine with helping. We'll take out the Plant's Control Room."

Niobe said " Ghost and I'll go after the Reactor itself. I hope we'll give you, Switch and the Keymaker enough time to get in the door."

Neo sighed and thought _'That's what worries me, if we don't have enough. If we fail it'll all be for nothing.' _He looked over as Morpheus spoke up " Trinity and I will be the back-up. We've got twelve hours before mid-night and the start of the plan. Does anyone have words that can't wait ? "

No one answered, Morpheus stood up rolled his stiff shoulder and the meeting finished. Neo winced as Morpheus did that wound was his fault, if Morpheus hadn't tried to save him the Captain wouldn't have gotten shot.

* * *

He couldn't get out of the room and down the hallway's ladder fast enough. Stress had gotten to him lately. First with the Bane-is really Smith-betrayal. Bane'd had almost identical blue eyes and manners as Smith. It had hurt, still did since it'd only been revealed to him yesterday. _' Dear God, I don't want to think about Smith. He manipulated me, claimed he loved me. Was probably lying when he did. I hope he won't ruin the plan.' _

The second was the Keymaker's plan to get into the Source, so many things could go wrong. If someone would be a second too late or a second too soon. They had to get in without getting killed first. He stopped as he saw the Neb's First-Mate Trinity, standing in front of his door. The blue-eyed woman looked up and asked " Is the meeting over Neo ? "

He felt a bit awkward as he replied " Yes, Trinity it is. Everything's been decided, Niobe and Ballard are going to help us tonight." He didn't know Trinity all that well. He was closer to Apoc and Switch, than he was Trinity and Morpheus.

Trinity smiled slightly " That's good, hopefully it'll be over tonight. You should rest for a bit, everyone else will be too." She walked past him to her room, he walked into his own. Neo groaned as he laid down on his worn-out bed and thought _'Please, let Trinity be right. Let it be over soon.'_


	3. Chapter 2 - Lupa

_Author's Note:_

This means its a Memory and the End of a memory.

* * *

**Lupa**

Some time later the long, black-haired man looked up as someone knocked on his door. Neo blinked and called "Come in." before brown-haired Lupa walked in. He hadn't seen the man in weeks. "Lupa ? What are you doing here ? I thought you were in Zion. "

Lupa smiled and sounded relieved " Hello again Neo, I'm so glad you're all right. Had me worried the search wouldn't end."

A confused reply from him "You were worried about me ? I thought Ballard was the only one looking for us. I mean, Niobe she only found us after recon."

" Yes, I was. I'm also on the Vigilant, we were the other crew sent looking. Speaking of Ballard, I saw him and Malachi but I haven't seen Bane around. Did something happen to him ? "

Neo bit his lip and twisted a strand of his hair as he thought _' So, Zion sent Ballard and Soren ?. Why ? Sure, I'm the 'only one' who can end the war, but they should worry about Zion. Not me, now what do I tell him about Bane ? I don't want to explain what Smith told me, but I don't want to lie. Tell the truth that he's dead. Just not that it wasn't the original Bane that died.' _

Then his own hesitant "Yeah, something did. Bane was... killed about a week ago. Morpheus told Ballard to go back to Zion, so they could have Bane's funeral. Ballard decided it would be better if they stayed to help us. In case the Squiddies came back."

The first time he ever saw a Sentinel flashed in his mind.

* * *

Memory, a year ago: He had been listening to Apoc talk about Zion. How it was humanity's last city, their very last hope when an alarm had gone off. Apoc said " Come on, Neo. Hopefully this'll be the last time you see one for a while."

He questioned " See one of what Apoc ? " as the older Rebel got up and walked out of the dining-room.

Neo thought _' See one of what ? I don't like this, but if he's calm. It can't be that bad, right ? ' _as he followed Apoc down the right-side of the hallway. Past the Mission Control Room, to a ladder he hadn't noticed before. Going up the ladder to the third level he saw that Morpheus and Trinity were sat in the cock-pit. The metal was still shining, unlike the rest of the Hover-craft and there was a... a blue hologram of something.

Then his gaze drifted up the wind-shield, to what was hovering just outside it. He stared frozen at the Machines. They looked like a floating hybrid of a metal squid and clawed spider. Covered in silver metal they had spider-like ruby eyes and thin pincers around their mouths. Along with eight squid-like tentacles that ended in claws or most did, he couldn't really tell. _' What the Hell are those ? Do I want to know ? No, no I don't. Let them go away, whatever they are.' _

Apoc pulled him down in a crouch and whispered " Those are Squiddies, Sentinels. Eitherway their killing machines, if they find Rebel 'crafts and sense movement or ... "

Trinity hissed " Apoc. Be quiet."

Neo held his breath as one of the Sentinels hovered closer to the Neb. It's red-eyes seemed to glare at them. The Sentinel tapped on the wind-shield with a claw. It made a high 'tiing'-ing sound as it hit the glass. He felt like he was going to pass out as another one floated up to the first. This one had sensor-dishs on two of its longest tentacles. _'Damn it, go away, go away. Please, I don't want to die.' _

A soft sigh of relief as the Machines floated away down the huge tunnel.

End of memory, present time

* * *

_' Those are the main threat to Zion's population if they get in. They're not we're going to defeat them first.' _

Neo startled as the other man asked " Why's everyone sticking around here then ? Shouldn't you be waiting in the defensive line with us later ? "

" The reason we're staying here is simple. It's because we've got a plan to stop the Machines. If it works we won't need that line to defend Zion."

There was a strange glint in Lupa's gray-eyes as the man nodded.

* * *

Neo couldn't help wondering what he thought. _'Is it relief that it'll finally be over ? Or does he like fighting the Machines ?'_


	4. Chapter 3 - Dark

**Dark**

Neo turned to look around at the dark forest, something felt off. Then he realized that the forest was completely silent, except for his own breath. He walked slowly as it started to rain. It dripped from the leaves into his hair and he shivered, remembered yesterday. Stared in shock at what he saw ... Smith and Switch. Heard his own alarmed cry of "Switch." She was tied up laying on the ground and Smith stood over her.

Her face was covered in blood, the blond woman blinked up at him and croaked "Neo, don't." He started to walk toward them, when Smith kicked her. Switch stifled a cry and he heard bone crack from the force.

Smith's icy-blue eyes flashed and he snarled "You worry about her. Her, Mr. Anderson."

He flinched at the old name, it'd been months since he'd heard that. _' It feels so odd hearing that, its not mine anymore. It never was.'_

* * *

Neo woke up to someone knocking on his door and felt relieved when Switch called "Neo, come on we've gotta get ready and get the Keymaker."

_'That was a weird night-mare. At least, at least Switch's fine. '_

Pushed himself up and replied as he got up "Okay, how much time do we have ? "

"Soon, everybody'll be ready, then we do our thing and wait until the Plant's shifts change. Until then we've got to get the Keymaker. "

_'Great, just what I've been waiting for. '_ he thought as he opened the door and walked out.

When Switch smiled it was grim " Yeah and its close the hotel."

He followed Switch up the ladder to the M.C.R. To see that Apoc, Morpheus and Trinity were waiting in the Matrix, Tank sat in the Operator's chair. He blinked as Tank smiled at him and asked "Ready, Neo ? "

He nodded and walked to his chair, pushed his hair back before he sat down and took a deep breath. Tank came over and said excitedly "Man, if tonight works. If it works we're partying tomorrow and you're my favourite person ever. "

_'I really didn't need that hanging over me too. Thanks Tank.'_

Neo winced more from Tank's sudden attitude shift then pain as he appeared in the Matrix.

* * *

He opened his eyes, as Switch appeared beside him, he tied his hair back. _' I really don't want it getting in the way tonight. We've got too many places to be at for me to leave it loose.' _Then they walked toward the door, Morpheus said "Good-luck with getting the Keymaker, we'll be waiting at the Layffette with the others."

As he and Switch walked out, it reminded him. They only had an hour before everyone would arrive for the meeting. When they got to the car, he got in the driver-seat and Switch sat beside him. She shook her head and asked "Why wouldn't he send Trinity with you ? This is too important for me."

He started driving before he replied "No, it's not Switch. Anyway, it's better you're with me. We're comfortable, Trinity and I not so much."

Switch laughed "Yeah, it's nice to know I've got more friends than just Apoc, you and Dozer."

_'I don't really wanna bring it up, but we've got twenty more minutes until we get there. Just do it.'_

"Switch ? " The white-haired woman nodded and he continued " Do you have any idea why Dozer and Tank avoid me ? Or Tank did until barely."

"Well, it's easy really, Neo. Until you came along we didn't have much hope of surviving. Plus, Morpheus was sure about you and wouldn't shut up. They got annoyed and figured you'd be friends with Morpheus and Trinity rather than Apoc and I. They were worried you'd turn arrogant like Cypher after he got freed. Well, Cypher had problems before he went bat-shit."

* * *

_'Did Morpheus do the same with him ? Expect when he found out Morpheus lied, he went and betrayed us ?. Dear God, that reminds me of Smith.'_

The dark voice snuck into his mind with _' "You missed me ? " _

Mentally, Neo hissed _'Smith, shut up and go away.' _

Mockingly, Smith stated _"You're an idiot to think you can stop this. A hundred years it has gone on and you think __**you **__can end it." _

He replied '_I will do it somehow, I will. Zion won't have to be afraid when its over. ' _As he shook Smith's voice out of his head, he noticed they were close to the Keymaker's hiding place.

* * *

Startled as Switch's voice broke in "Are you all right Neo ? You just pulled some odd faces for a while. "

"Sorry, I got distracted. Should we stop here ? "

"Sure."

He left the engine on and they got out, walked up to a shabby, dark-gray two-storey house. He didn't like it something was wrong. Then Neo looked up the street, to see that a silver car was parked ahead of them, " I think Frenchie's twins are here or someone else is. "

Switch replied as they walked in "Let's say "Hi." shall we ? "

* * *

Neo grinned slightly, before he calmed down. Ready to fight for the Key-maker.


	5. Chapter 4 - Keys

**Keys**

Neo looked around the inside of the house, light-walls and a dark-wooded stair-case. The Keymaker's voice shouted "Help !." from the second level. His vision flickered into code and he saw the old man with a blond Were-wolf and pinned by a red-haired Vamp.

He ran up the stairs as the Were growled " You're going back, old man. There's no stupid pretty-boy to save you now."

He hissed "Whoever you are. I am not pretty." _'Damn it I'm not.' _while he jump-kicked the Were in the back. Blondie went flying and crashed through the wall.

Neo heard "My keys, I lost my keys." from the Keymaker, while the Vamp lunged at him. He jumped above the Vamp and twisted out of Blondie's reach. As he landed the Vamp slammed into his back, he rolled over. Got up and kicked the red-head and shouted "How'd we get rid of 'em ? ".

No answer from the old program. He'd thought _'At least, they aren't damned mutant ants this time. Wait, Niobe said Vamp code can be stopped with a stake.' _The Keymaker had disappeared from his sight. Neo leaned down, grabbed, twisted and threw the Vamp into the stair-railing. Meanwhile, Blondie had changed into a bi-pedal, yellow-furred wolf and gone after Switch.

* * *

He ran, jumped and flipped off the landing before he turned in mid-air and landed on his feet. The Keymaker had gotten pinned in the living-room by a tall, brown-haired program. For a second it wasn't a random program, it was Smith. He stared and forgot to breath, _'It's not him, even if it was he doesn't care. '._ Frozen for that second Neo got floored by the Vamp. Thankfully, the illusion of Smith had disappeared as well.

_'Balroan Hells, damn it we don't have time for all this fighting.'_

The Vamp glared and hissed at him, until he surprised it by throwing it into a table_._ Then the Keymaker called "I've got my keys. Find me a locked door and we're out of here." Neo turned his head, to see the brown-haired program was sense-less on the floor. _' How did that happen ? I thought he didn't know how to fight. ' _

Switch exclaimed "There's none up here !. They all have dead-bolts. Neo, can you find any ? "

He got up, rushed past the Keymaker, across the living-room and into the kitchen.

* * *

Then looked around for a back-door. He called back "There's nothing. How can there not be any ?"

The Keymaker "What about the front ? Just lock it. " At those words Neo felt like running **into **a wall, not up it.

Switch called a few moments later "I got it." He felt relieved, rushed out and round-house kicked the Vamp. Who'd been sneaking up on the old program.

Said program turned to look at him " You didn't have to do that... oh, well. Let's get out of here."

_'He's crazy, the old program's crazy that Vamp would've killed him.'_

He shook his head and followed the old man to the door. Stared as it was unlocked to reveal not the street, but the inside of the Lafayette hotel. They walked in and Switch asked "What about the car ? "

"I forgot all about it. There's no time now." Neo shrugged and walked up to the meeting-room.

* * *

He hoped the meeting would be quick.


	6. Chapter 5 - Wait

_Author's_ Note: Lots of speech in this chapter and maybe the next.

* * *

**Wait**

Neo, Switch and the Keymaker walked into the meeting-room. He felt the nervous excitement coming from the waiting Rebels. He looked around at the old, green-walled room. There were a few padded chairs scattered around. One was white, the other green, and the last was a familiar red one. The same one from a year ago when he'd been freed.

Niobe sat in the white one with Ghost standing beside her on the right. Ballard sat in the green with Malachi on the left, and Morpheus in the red with Trinity on the right. Apoc was standing on the left side of Morpheus, he and Switch moved to stand with their friend. He watched as the Keymaker walked to stand by Niobe and Ghost.

* * *

Then Niobe said, brightly "Switch, Neo. Nice to see you two again."

He smiled at his other friend "You too Niobe, Ghost." as he nodded to Ballard and Morpheus.

Niobe continued a second later "So, you're the Keymaker, I've heard so much about. The one who came up with this plan."

The Keymaker responded "Yes, I am. You need to remember you only have five minutes to set the bomb in the Reactor and get out."

Niobe smiled and replied "I know, but I like challenges. It wouldn't be one if I didn't have a time to beat."

Neo jumped as Morpheus cleared his throat and turned to look at the dark man. His Captain's gaze moved, slowly, around the room. Neo shivered as it stopped on him.

* * *

Morpheus asked, suddenly "Do you all believe that the war will end tonight ?"

_'Believe it, yes. Yes, it's the only thing keeping me sane... besides the adrenaline.'_

He and the others responded "Yes."

"Our hope stands on the edge of oblivion, do you **truly** believe it ?."

They all exclaimed "Yes!."

Morpheus continued "You all know we only have a limited time to pull off this plan. The worst part you face now that the time has finally come. That is knowing you and every single one of your friends could die tonight. So, tell me now is your own life and your friends lives, are they worth giving up for the sake of humanity's freedom ?. "

_'My life for Zion, for all of humanity of course it is. We've done everything to save them, waited bleeding and hoping to bring them peace someday. We'd do anything, even give up our friends to end it. Everything I've done in this war was for my friends or my love. No matter how stupid my choice of a love is, was. Damn it, I don't know what to think of him.'_

He answered "Everything we've ever done is for all of them. It's what we've lived for, what's let us get through it all." as Morpheus stood up and paced.

Then his Captain asked " Every drop of blood ? Every bit of pain you've experienced since you became free ? Absolutely everything, are you sure ?. "

Neo shifted, the adrenaline hadn't faded yet. He wanted to do something, waited to finally go. He was distracted briefly as he saw Apoc and Switch nod in agreement. He wondered briefly how many friends they had lost. Everyone else had started to look impatient too, even the Keymaker.

_'All the more reason to end this damned thing. Yes, absolutely that mean's there was a reason for my guilt about the real Bane's death by Smith. I wish I'd actually talked to him for more than a few seconds. I would have known it was Smith not Bane. Either way, everything'll be worth it tonight.' _

He noticed as Ghost shifted by Niobe's chair and the Logos' First-Mate replied " Every time we've gotten injured or nearly died while saving someone. No matter who it was, we were building our inner strength up."

Malachi interjected "Yeah, we wouldn't think of doing this otherwise. We'd be running away instead. All our friends are counting on us, it's like we were... " Malachi trailed off.

Morpheus smiled and launched into an excited speech "Like this is our fate or our destiny to be here ?. My friends, I believe everything has lead us to this. Our shared experiences have brought us together now. The bad even more than the good. Why is that ? Simply put without the strength of our friends and their support ... in the worst of situations we would have died. We are stronger than the Machines. The Machines work together because they have to, not because they want to. Unlike them we are united by choice. This is the night we've waited for. Tonight we will end this war once and for all. "

* * *

Neo grinned and cheered with the others. Around him the others started to talk. Morpheus looked at him and Switch, then nodded. _'We can finally get going. Thank God, I couldn't stand waiting any longer.' _

He pulled his shades out, surprised they were still in one piece. He laughed again and put them on. Switch pulled her own shades on. Then he, Switch and the Keymaker walked toward the door.

He heard everyone wish them "Good-luck." as they stopped in front of it. The Keymaker locked then unlocked and opened it. Neo thought _' We've got thirty minutes to take out the guards. Once and for all, no more waiting. No time for more worrying, until we get in the Source hallway at least.' _as he took a deep breath to try and wait out the adrenaline. It didn't work.

Then the two Rebels and program walked into the Source building.


	7. Chapter 6 - SWAT

_Author's Note :_ Thanks to _blackcat21223_ for the favourites.

* * *

**SWAT**

Neo walked out into the open with Switch. They had to get from the twenty-second floor to the forty-second without missing any of the guards. They absolutely couldn't get interrupted by Agents. His vision changed into code and he saw four guards farther up ahead. Nodded to the woman in white, then ran along the wall to jump off and kicked the closest one in the face. Flipped over as Switch punched the one nearest to her, he landed and grabbed, then threw the farthest one into the wall. Switch kicked the last one as the Key-maker walked into the hall-way.

Ran ahead to the next level, hissed as he saw a few SWAT members standing down the hall from him. He recognized the Captain, the guy who had shot him in the shoulder when...before, before he'd been killed. His shoulder twitched as he remembered the pain. _'He's going down he wanted to kill everyone. Not that I would've minded if he'd killed Cypher the bastard. Still he can't get away again, I wish Morpheus would've let us have guns. Of course he's right, they'd have made too much noise.'_

Needed to take out their shields before Switch would have a good opportunity to get in. Crept down the hall believing he wouldn't be seen, until he was behind one of them. Grabbed the nearest SWAT and threw him into the others, they fell to the floor. Punched the Captain who was getting up as Switch swept into the fight. Angry recognition in the man's gray-eyes as the Captain blocked his kick. Surprised to find himself falling as the SWAT tackled him. They rolled over a few times before his shoulder smacked into the wall. Hissed as he got punched in the face, Switch was suddenly choking the man into unconsciousness.

"C'mon, Neo. We don't have time for draw-outs remember."

All the fights blurred into one huge confusing mess.

* * *

As soon as they stepped onto the forty-third floor the fights stopped all together. _'Don't tell me they'll have Agents' waiting for us.' _

Switch and himself scanned all the rooms on the floors before they'd let the Key-maker on it. Neo'd barely caught his breath as the city's lights started to go out and turned for the door. It looked just like all the other doors but apparently it had to be this door. The Key-maker asked as he unlocked the door "Are you ready ?"

Switch replied "As we'll ever be, let's go."

Another surge of adrenalin as he entered the white, green-doored hallway. _'Only twenty more minutes and the war should be over. Still this is way too easy. It was just SWAT, not a single Agent. I don't like this at all.'_

His adrenalin soon turned to impatience as the hall-ways all looked the same. Both of the Rebels asked simultaneously "How much farther ?"

An answer of "Just a little bit." as they turned around a corner like all the others.

Neo's throat felt tight as his heart tried to beat through it. Smith smiled at him "Hello, love."


End file.
